Molecular models of the action potential channel, interleukin 2, Delta hemolysin, and Alpha toxin were developed. This was done by analyzing their sequences using methods previously developed to predict which portions of Alpha helices and Beta strands should be exposed to water, other protein segments, or in membranes to hydrocarbon lipid chains. The method was also used to analyze possible homologies of distantly related proteins. An interesting finding is that one face of an amphipathic Alpa helix appears to be conserved in human granulocyte-macrophage colony stimulating factor, somatotrophin, lactogen, and the Epsilon peptide of insulin-like growth factor II. The globin superfamily of sequences, as a prototype of helical proteins, was analyzed to learn which aspects of their structures were most conserved, as well as to determine, on such basis, the relationships between distantly related globin sequences. The most conserved parameter is the partition energy for moving Alpha helical segments from water to their optimal positions at the water-protein interface. The study indicated that leghemoglobins are almost equally related to vertebrate and invertebrate globins, therefore, suggesting an evolutionary branch from these globins corresponding to the origin of animals from plants.